Population data for insertion/deletion markers.

<p>Panels 1, 2 and 3 consist of approximately 18 target indels each, and are outlined in detail in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052750#pone.0052750.s004" target="_blank">Table S1</a>.</p

Concordance of 24 tumor/normal matched pairs.

*<p>Poor amplification for these samples.</p

An overview of the experimental design and procedure.

<p><b>A</b> shows the role of the selector probe and complementary vector. The target DNA fragment containing the insertion/deletion is cut with restriction enzymes and ligated to a complementary probe to form a circle. The circular ligation product is again cut to form a linear fragment with universal primer binding site. <b>B</b> shows the MLGA reaction scheme. Genomic DNA is restriction digested; ligated to specific selector probes and these products are amplified by multiplex PCR using fluorescent labels. The fragments can then be separated by capillary electrophoresis and analyzed. <b>C</b> is a schematic representation of the process, from design to analysis.</p

CNV plot showing detected copy number alterations in <i>RAG1</i> (patient 534, panel A) and <i>XIAP</i> (patient 523, panel B).

<p>CNV plot showing detected copy number alterations in <i>RAG1</i> (patient 534, panel A) and <i>XIAP</i> (patient 523, panel B).</p

Number of reads, average read depth, coverage and specificity values per. patient.

a<p>Av. Read depth is the average number of reads obtained per position in the targeted region.</p>b<p>F_1x =  fraction of targeted region covered by at least 1 read.</p>c<p>Fc_20x  =  fraction of captured fragments covered by at least 20 reads.</p><p>Number of reads, average read depth, coverage and specificity values per. patient.</p

Mutations detected in patients with unknown disease causing variant.

<p>A clinical phenotype was reported as follows: EGS538 and 550 have symptoms and signs compatible with STAT3 mutations, including increased IgE-levels and <i>S. aureus</i> infections. Prior to the analysis EGS539 and 540 had 6% and <1% B-lymphocytes in peripheral blood and an increased susceptibility to bacterial infections. EGS542 has been prone to bacterial infections since childhood. EGS543, 546–548, 554, 555, 557 and 559 have reduced levels of B-lymphocytes and of immunoglobulins. EGS560 has a clinical phenotype related to common variable immunodeficiency, but also has congenital defects affecting non-lymphoid organs.</p>a<p>(Potentially) causal mutations are listed in bold.</p>b<p>Patient diagnosed with asplenia. Candidate genes not included in this assay.</p>c<p>No potential causing variants were found for these individuals in the NGS data</p>d<p>Manuscript in preparation.</p><p>Mutations detected in patients with unknown disease causing variant.</p

SNV, indel and CNV detection in patients with known causal mutation(s).

<p>Abbreviations: NGS: Next Generation Sequencing; CNV: Copy Number Variant</p><p>SNV, indel and CNV detection in patients with known causal mutation(s).</p